PAGA embeddings

Import Seurat as adata

PCA

Neighbor graph

Denoise neighbor graph

PAGA on leiden graph

Cluster marker

HSCs: Procr
Erythroids: Gata1, Klf1, Epor, Gypa, Hba-a2, Hba-1, Spi1
Neutrophils: Elane, Cebpe, Ctsg, Mpo, Gfi1
Monocytes: Irf8, Csf1r, Ctsg, Mpo
Megakaryocytes: Itga2b (encodes protein CD41), Pbx1, Sdpr, Vwf
Basophils: Mcpt8, Prss34
B cells: Cd19, Vpreb2, Cd79a
Mast cells: Cma1, Gzmb, c-kit
Mast cells & Basophils: Ms4a2, Fcer1a, Cpa3

PAGA graph (NaCl)

PAGA graph (CpG)

PAGA cell embeddings

Embeddings (NaCl)

Embeddings (CpG)

RNA velocity

Import velocyto loom

Subset data

Filter and normalize

Compute RNA velocity

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